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Ma XQ, Wang B, Wei W, Tan FC, Su H, Zhang JZ, Zhao CY, Zheng HJ, Feng YQ, Shen W, Yang JB, Li FL. Alginate oligosaccharide assimilation by gut microorganisms and the potential role in gut inflammation alleviation. Appl Environ Microbiol 2024; 90:e0004624. [PMID: 38563787 PMCID: PMC11107165 DOI: 10.1128/aem.00046-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Dietary fiber metabolism by gut microorganisms plays important roles in host physiology and health. Alginate, the major dietary fiber of daily diet seaweeds, is drawing more attention because of multiple biological activities. To advance the understanding of alginate assimilation mechanism in the gut, we show the presence of unsaturated alginate oligosaccharides (uAOS)-specific alginate utilization loci (AUL) in human gut microbiome. As a representative example, a working model of the AUL from the gut microorganism Bacteroides clarus was reconstructed from biochemistry and transcriptome data. The fermentation of resulting monosaccharides through Entner-Doudoroff pathway tunes the metabolism of short-chain fatty acids and amino acids. Furthermore, we show that uAOS feeding protects the mice against dextran sulfate sodium-induced acute colitis probably by remodeling gut microbiota and metabolome. IMPORTANCE Alginate has been included in traditional Chinese medicine and daily diet for centuries. Recently discovered biological activities suggested that alginate-derived alginate oligosaccharides (AOS) might be an active ingredient in traditional Chinese medicine, but how these AOS are metabolized in the gut and how it affects health need more information. The study on the working mechanism of alginate utilization loci (AUL) by the gut microorganism uncovers the role of unsaturated alginate oligosaccharides (uAOS) assimilation in tuning short-chain fatty acids and amino acids metabolism and demonstrates that uAOS metabolism by gut microorganisms results in a variation of cell metabolites, which potentially contributes to the physiology and health of gut.
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Affiliation(s)
- Xiao-Qing Ma
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Bing Wang
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wei
- Innovation Center of Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fang-Cheng Tan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Hang Su
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jun-Zhe Zhang
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chen-Yang Zhao
- Innovation Center of Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yan-Qin Feng
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jin-Bo Yang
- Innovation Center of Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fu-Li Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
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Zhang YS, Zhang YQ, Zhao XM, Liu XL, Qin QL, Liu NH, Xu F, Chen XL, Zhang YZ, Li PY. Metagenomic insights into the dynamic degradation of brown algal polysaccharides by kelp-associated microbiota. Appl Environ Microbiol 2024; 90:e0202523. [PMID: 38259074 PMCID: PMC10880675 DOI: 10.1128/aem.02025-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Marine bacteria play important roles in the degradation and cycling of algal polysaccharides. However, the dynamics of epiphytic bacterial communities and their roles in algal polysaccharide degradation during kelp decay are still unclear. Here, we performed metagenomic analyses to investigate the identities and predicted metabolic abilities of epiphytic bacterial communities during the early and late decay stages of the kelp Saccharina japonica. During kelp decay, the dominant epiphytic bacterial communities shifted from Gammaproteobacteria to Verrucomicrobia and Bacteroidetes. In the early decay stage of S. japonica, epiphytic bacteria primarily targeted kelp-derived labile alginate for degradation, among which the gammaproteobacterial Vibrionaceae (particularly Vibrio) and Psychromonadaceae (particularly Psychromonas), abundant in alginate lyases belonging to the polysaccharide lyase (PL) families PL6, PL7, and PL17, were key alginate degraders. More complex fucoidan was preferred to be degraded in the late decay stage of S. japonica by epiphytic bacteria, predominantly from Verrucomicrobia (particularly Lentimonas), Pirellulaceae of Planctomycetes (particularly Rhodopirellula), Pontiellaceae of Kiritimatiellota, and Flavobacteriaceae of Bacteroidetes, which depended on using glycoside hydrolases (GHs) from the GH29, GH95, and GH141 families and sulfatases from the S1_15, S1_16, S1_17, and S1_25 families to depolymerize fucoidan. The pathways for algal polysaccharide degradation in dominant epiphytic bacterial groups were reconstructed based on analyses of metagenome-assembled genomes. This study sheds light on the roles of different epiphytic bacteria in the degradation of brown algal polysaccharides.IMPORTANCEKelps are important primary producers in coastal marine ecosystems. Polysaccharides, as major components of brown algal biomass, constitute a large fraction of organic carbon in the ocean. However, knowledge of the identities and pathways of epiphytic bacteria involved in the degradation process of brown algal polysaccharides during kelp decay is still elusive. Here, based on metagenomic analyses, the succession of epiphytic bacterial communities and their metabolic potential were investigated during the early and late decay stages of Saccharina japonica. Our study revealed a transition in algal polysaccharide-degrading bacteria during kelp decay, shifting from alginate-degrading Gammaproteobacteria to fucoidan-degrading Verrucomicrobia, Planctomycetes, Kiritimatiellota, and Bacteroidetes. A model for the dynamic degradation of algal cell wall polysaccharides, a complex organic carbon, by epiphytic microbiota during kelp decay was proposed. This study deepens our understanding of the role of epiphytic bacteria in marine algal carbon cycling as well as pathogen control in algal culture.
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Affiliation(s)
- Yi-Shuo Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Qi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiang-Ming Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Lei Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Joint Research Center for Marine Microbiol Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Joint Research Center for Marine Microbiol Science and Technology, Shandong University and Ocean University of China, Qingdao, China
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Cha QQ, Liu SS, Dang YR, Ren XB, Xu F, Li PY, Chen XL, Wang P, Zhang XY, Zhang YZ, Qin QL. Ecological function and interaction of different bacterial groups during alginate processing in coastal seawater community. ENVIRONMENT INTERNATIONAL 2023; 182:108325. [PMID: 37995388 DOI: 10.1016/j.envint.2023.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023]
Abstract
The degradation of high molecular weight organic matter (HMWOM) is a core process of oceanic carbon cycle, which is determined by the activity of microbial communities harboring hundreds of different species. Illustrating the active microbes and their interactions during HMWOM processing can provide key information for revealing the relationship between community composition and its ecological functions. In this study, the genomic and transcriptional responses of microbial communities to the availability of alginate, an abundant HMWOM in coastal ecosystem, were elucidated. The main degraders transcribing alginate lyase (Aly) genes came from genera Alteromonas, Psychrosphaera and Colwellia. Meanwhile, some strains, mainly from the Rhodobacteraceae family, did not transcribe Aly gene but could utilize monosaccharides to grow. The co-culture experiment showed that the activity of Aly-producing strain could promote the growth of Aly-non-producing strain when alginate was the sole carbon source. Interestingly, this interaction did not reduce the alginate degradation rate, possibly due to the easily degradable nature of alginate. This study can improve our understanding of the relationship between microbial community activity and alginate metabolism function as well as further manipulation of microbial community structure for alginate processing.
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Affiliation(s)
- Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Sha-Sha Liu
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China; MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
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Qi J, Zhou Q, Huang D, Yu Z, Meng F. Construction of synthetic anti-fouling consortia: fouling control effects and polysaccharide degradation mechanisms. Microb Cell Fact 2023; 22:230. [PMID: 37936187 PMCID: PMC10631183 DOI: 10.1186/s12934-023-02235-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
The physical states and chemical components of bulk sludge determine the occurrence and development of membrane fouling in membrane bioreactors. Thus, regulation of sludge suspensions can provide new strategies for fouling control. In this study, we used "top-down" enrichment to construct a synthetic anti-fouling consortium (SAC) from bio-cake and evaluate its roles in preventing membrane fouling. The SAC was identified as Massilia-dominated and could almost wholly degrade the alginate solution (1,000 mg/L) within 72 h. Two-dimensional Fourier transformation infrared correlation spectroscopy (2D-FTIR-CoS) analysis demonstrated that the SAC induced the breakage of glycosidic bond in alginates. The co-cultivation of sludge with a low dosage of SAC (ranging from 0 to 1%) led to significant fouling mitigation, increased sludge floc size, and decreased unified membrane fouling index value (0.55 ± 0.06 and 0.11 ± 0.05). FTIR spectra and X-ray spectroscopy analyses demonstrated that the addition of SAC decreased the abundance of the O-acetylation of polysaccharides in extracellular polymeric substances. Secondary derivatives analysis of amide I spectra suggested a strong reduction in the α-helix/(β-sheet + random coil) ratio in the presence of SAC, which was expected to enhance cell aggregation. Additionally, the extracellular secretions of SAC could both inhibit biofilm formation and strongly disperse the existing biofilm strongly during the biofilm incubation tests. In summary, this study illustrates the feasibility and benefits of using SAC for fouling control and provides a new strategy for fouling control.
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Affiliation(s)
- Ji Qi
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Qicheng Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Danlei Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China.
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Rønne ME, Tandrup T, Madsen M, Hunt CJ, Myers PN, Moll JM, Holck J, Brix S, Strube ML, Aachmann FL, Wilkens C, Svensson B. Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate. Appl Environ Microbiol 2023; 89:e0118523. [PMID: 37791757 PMCID: PMC10617595 DOI: 10.1128/aem.01185-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 10/05/2023] Open
Abstract
Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.
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Affiliation(s)
- Mette E. Rønne
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tobias Tandrup
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikkel Madsen
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Cameron J. Hunt
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pernille N. Myers
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Janne M. Moll
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael L. Strube
- Department of Biotechnology and Biomedicine, Bacterial Ecophysiology and Biotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Finn L. Aachmann
- Department of Biotechnology and Food Science, Norwegian Biopolymer Laboratory (NOBIPOL), NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Structural Enzymology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
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Peña-Castro JM, Muñoz-Páez KM, Robledo-Narvaez PN, Vázquez-Núñez E. Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion. Microorganisms 2023; 11:2197. [PMID: 37764041 PMCID: PMC10535843 DOI: 10.3390/microorganisms11092197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.
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Affiliation(s)
- Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico;
| | - Karla M. Muñoz-Páez
- CONAHCYT—Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Queretaro 76230, Queretaro, Mexico;
| | | | - Edgar Vázquez-Núñez
- Grupo de Investigación Sobre Aplicaciones Nano y Bio Tecnológicas para la Sostenibilidad (NanoBioTS), Departamento de Ingenierías Química, Electrónica y Biomédica, División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, Lomas del Campestre, León 37150, Guanajuato, Mexico
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Mannuronate C-5 epimerases and their use in alginate modification. Essays Biochem 2023; 67:615-627. [PMID: 36876890 DOI: 10.1042/ebc20220151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
Alginate is a polysaccharide consisting of β-D-mannuronate (M) and α-L-guluronate (G) produced by brown algae and some bacterial species. Alginate has a wide range of industrial and pharmaceutical applications, owing mainly to its gelling and viscosifying properties. Alginates with high G content are considered more valuable since the G residues can form hydrogels with divalent cations. Alginates are modified by lyases, acetylases, and epimerases. Alginate lyases are produced by alginate-producing organisms and by organisms that use alginate as a carbon source. Acetylation protects alginate from lyases and epimerases. Following biosynthesis, alginate C-5 epimerases convert M to G residues at the polymer level. Alginate epimerases have been found in brown algae and alginate-producing bacteria, predominantly Azotobacter and Pseudomonas species. The best characterised epimerases are the extracellular family of AlgE1-7 from Azotobacter vinelandii (Av). AlgE1-7 all consist of combinations of one or two catalytic A-modules and one to seven regulatory R-modules, but even though they are sequentially and structurally similar, they create different epimerisation patterns. This makes the AlgE enzymes promising for tailoring of alginates to have the desired properties. The present review describes the current state of knowledge regarding alginate-active enzymes with focus on epimerases, characterisation of the epimerase reaction, and how alginate epimerases can be used in alginate production.
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Cao S, Li L, Li Q, Jiang L, Zhu B, Yao Z. A novel alginate lyase and its domain functions for the preparation of unsaturated monosaccharides. Appl Microbiol Biotechnol 2023; 107:1737-1749. [PMID: 36795142 DOI: 10.1007/s00253-023-12424-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/30/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Brown algae are considered promising crops for the production of sustainable biofuels. However, the commercial application has been limited by lack of efficient methods for converting alginate into fermentable sugars. Herein, we cloned and characterized a novel alginate lyase AlyPL17 from Pedobacter hainanensis NJ-02. It possessed outstanding catalytic efficiency toward polymannuronic acid (polyM), polyguluronic acid (polyG), and alginate sodium, with kcat of 39.42 ± 1.9 s-1, 32.53 ± 0.88 s-1, and 38.30 ± 2.12 s-1, respectively. AlyPL17 showed maximum activity at 45 °C and pH 9.0. The domain truncation did not change the optimal temperature and optimal pH, but greatly reduced the activity. In addition, AlyPL17 degrades alginate through the cooperative action of two structural domains in an exolytic mode. The minimal degradation substrate of AlyPL17 is a disaccharide. Furthermore, AlyPL17 and AlyPL6 can synergistically degrade alginate to prepare unsaturated monosaccharides that can be converted to 4-deoxy-L-erythron-5-hexoseuloseuronate acid (DEH). DEH is reduced to KDG by DEH reductase (Sdr), which enters the Entner-Doudoroff (ED) pathway as a common metabolite and is converted to bioethanol. KEY POINTS: • Biochemical characterization of alginate lyase from Pedobacter hainanensis NJ-02 and its truncated form. • Degradation patterns of AlyPL17 and the role of its domains in product distribution and mode of action. • Potential of synergistic degradation system for efficient preparation of unsaturated monosaccharides.
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Affiliation(s)
- Shengsheng Cao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Li Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Qian Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China.
| | - Zhong Yao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China
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Characterization of Multiple Alginate Lyases in a Highly Efficient Alginate-Degrading Vibrio Strain and Its Degradation Strategy. Appl Environ Microbiol 2022; 88:e0138922. [PMID: 36409133 PMCID: PMC9746302 DOI: 10.1128/aem.01389-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Alginate is an important polysaccharide in the ocean that supports the growth of marine microorganisms. Many widespread Vibrio species possess alginate lyases and can utilize alginate as a carbon source, but the detailed alginate degradation mechanism in Vibrio remains to be further explored. In this study, we obtained a highly efficient alginate-degrading strain, Vibrio pelagius WXL662, with 11 alginate lyases (VpAly-I to -XI) and further elucidated its molecular mechanism of alginate degradation. Three alginate utilization loci (AUL) were identified in different parts of WXL662's genome, comprising six alginate lyases (VpAly-I, -II, -VIII, -IX, -X, and -XI) and other genes related to alginate degradation. Most of the alginate-degrading genes are strongly induced when alginate is provided as the sole carbon source. Ten alginate lyases (VpAly-I to -X) had been purified and characterized, including six from polysaccharide lyase family 7 (PL7), three from PL17, and one from PL6. These recombinant alginate lyases existing in different cellular locations were active at a wide temperature (10 to 50°C) and pH (4.0 to 9.0) range, with different substrate preferences and diverse degradation products, enabling WXL662 to efficiently utilize alginate in a changing marine environment. Importantly, outer membrane vesicles (OMVs) can act as vectors for alginate lyases (VpAly-II, -V, and -VI) in WXL662. Further investigations of public Vibrio genomes revealed that most alginate-degrading vibrios possess one AUL instead of previously reported "scattered" system. These results emphasize the specific alginate degradation strategy in Vibrio pelagius WXL662, which can be used as a model strain to study the ecological importance of effective alginate-degrading vibrios in the ocean. IMPORTANCE Alginate is an important carbon source in the marine environment, and vibrios are major alginate utilizers. Previous studies focused only on the characteristics of individual alginate lyases in vibrios, but few of them discussed the comprehensive alginate-degrading strategy. Here, we depicted the alginate utilization mechanism and its ecological implications of a highly efficient alginate-degrading Vibrio strain, WXL662, which contained 11 alginate lyases with distinct enzymatic characteristics. Importantly, unlike other vibrios with only one alginate utilization locus (AUL) or the previously reported "scattered" system, three AUL were identified in WXL662. Additionally, the involvement of outer membrane vesicles (OMVs) in the secretion of alginate lyases is proposed for the first time.
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10
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Bligh M, Nguyen N, Buck-Wiese H, Vidal-Melgosa S, Hehemann JH. Structures and functions of algal glycans shape their capacity to sequester carbon in the ocean. Curr Opin Chem Biol 2022; 71:102204. [PMID: 36155346 DOI: 10.1016/j.cbpa.2022.102204] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023]
Abstract
Algae synthesise structurally complex glycans to build a protective barrier, the extracellular matrix. One function of matrix glycans is to slow down microorganisms that try to enzymatically enter living algae and degrade and convert their organic carbon back to carbon dioxide. We propose that matrix glycans lock up carbon in the ocean by controlling degradation of organic carbon by bacteria and other microbes not only while algae are alive, but also after death. Data revised in this review shows accumulation of algal glycans in the ocean underscoring the challenge bacteria and other microbes face to breach the glycan barrier with carbohydrate active enzymes. Briefly we also update on methods required to certify the uncertain magnitude and unknown molecular causes of glycan-controlled carbon sequestration in a changing ocean.
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Affiliation(s)
- Margot Bligh
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Nguyen Nguyen
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Hagen Buck-Wiese
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany.
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11
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Jiang WX, Li PY, Chen XL, Zhang YS, Wang JP, Wang YJ, Sheng Q, Sun ZZ, Qin QL, Ren XB, Wang P, Song XY, Chen Y, Zhang YZ. A pathway for chitin oxidation in marine bacteria. Nat Commun 2022; 13:5899. [PMID: 36202810 PMCID: PMC9537276 DOI: 10.1038/s41467-022-33566-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Oxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)-2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH3 via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria.
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Affiliation(s)
- Wen-Xin Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yi-Shuo Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Ping Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yan-Jun Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yin Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
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12
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Petersen AB, Christensen IA, Rønne ME, Stender EGP, Teze D, Svensson B, Aachmann FL. 1H, 13C, 15N resonance assignment of the enzyme KdgF from Bacteroides eggerthii. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:343-347. [PMID: 36042150 PMCID: PMC9510102 DOI: 10.1007/s12104-022-10102-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
To fully utilize carbohydrates from seaweed biomass, the degradation of the family of polysaccharides known as alginates must be understood. A step in the degradation of alginate is the conversion of 4,5-unsaturated monouronates to 4-deoxy-L-erythro-5-hexoseulose catalysed by the enzyme KdgF. In this study BeKdgF from Bacteroides eggerthii from the human gut microbiota has been produced isotopically labelled in Escherichia coli. Here the 1H, 13C, and 15N NMR chemical shift assignment for BeKdgF is reported.
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Affiliation(s)
- Agnes Beenfeldt Petersen
- Department of Chemistry, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Idd Andrea Christensen
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Mette E Rønne
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Emil G P Stender
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - David Teze
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Finn Lillelund Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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13
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Dobruchowska JM, Bjornsdottir B, Fridjonsson OH, Altenbuchner J, Watzlawick H, Gerwig GJ, Dijkhuizen L, Kamerling JP, Hreggvidsson GO. Enzymatic depolymerization of alginate by two novel thermostable alginate lyases from Rhodothermus marinus. FRONTIERS IN PLANT SCIENCE 2022; 13:981602. [PMID: 36204061 PMCID: PMC9530828 DOI: 10.3389/fpls.2022.981602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Alginate (alginic acid) is a linear polysaccharide, wherein (1→4)-linked β-D-mannuronic acid and its C5 epimer, α-L-guluronic acid, are arranged in varying sequences. Alginate lyases catalyze the depolymerization of alginate, thereby cleaving the (1→4) glycosidic linkages between the monomers by a β-elimination mechanism, to yield unsaturated 4-deoxy-L-erythro-hex-4-enopyranosyluronic acid (Δ) at the non-reducing end of resulting oligosaccharides (α-L-erythro configuration) or, depending on the enzyme, the unsaturated monosaccharide itself. In solution, the released free unsaturated monomer product is further hydrated in a spontaneous (keto-enol tautomerization) process to form two cyclic stereoisomers. In this study, two alginate lyase genes, designated alyRm3 and alyRm4, from the marine thermophilic bacterium Rhodothermus marinus (strain MAT378), were cloned and expressed in Escherichia coli. The recombinant enzymes were characterized, and their substrate specificity and product structures determined. AlyRm3 (PL39) and AlyRm4 (PL17) are among the most thermophilic and thermostable alginate lyases described to date with temperature optimum of activity at ∼75 and 81°C, respectively. The pH optimum of activity of AlyRm3 is ∼5.5 and AlyRm4 at pH 6.5. Detailed NMR analysis of the incubation products demonstrated that AlyRm3 is an endolytic lyase, while AlyRm4 is an exolytic lyase, cleaving monomers from the non-reducing end of oligo/poly-alginates.
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Affiliation(s)
- Justyna M. Dobruchowska
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | | | | | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Stuttgart, Germany
| | | | - Gerrit J. Gerwig
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Johannis P. Kamerling
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Gudmundur O. Hreggvidsson
- Matís Ltd., Reykjavík, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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14
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Production of 4-Deoxy-L-erythro-5-Hexoseulose Uronic Acid Using Two Free and Immobilized Alginate Lyases from Falsirhodobacter sp. Alg1. Molecules 2022; 27:molecules27103308. [PMID: 35630785 PMCID: PMC9144776 DOI: 10.3390/molecules27103308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023] Open
Abstract
Falsirhodobacter sp. alg1 expresses two alginate lyases, AlyFRA and AlyFRB, to produce the linear monosaccharide 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH) from alginate, metabolizing it to pyruvate. In this study, we prepared recombinant AlyFRA and AlyFRB and their immobilized enzymes and investigated DEH production. Purified AlyFRA and AlyFRB reacted with sodium alginate and yielded approximately 96.8% DEH. Immobilized AlyFRA and AlyFRB were prepared using each crude enzyme solution and κ-carrageenan, and immobilized enzyme reuse in batch reactions and DEH yield were examined. Thus, DEH was produced in a relatively high yield of 79.6%, even after the immobilized enzyme was reused seven times. This method can produce DEH efficiently and at a low cost and can be used to mass produce the next generation of biofuels using brown algae.
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15
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Li Z, Huang X, Guo Y, Zhang C, Yang L, Du X, Ni H, Wang X, Zhu Y. Toward Understanding the Alginate Catabolism in Microbulbifer sp. ALW1 by Proteomics Profiling. Front Bioeng Biotechnol 2022; 10:829428. [PMID: 35372316 PMCID: PMC8967155 DOI: 10.3389/fbioe.2022.829428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain of Microbulbifer sp. ALW1 has demonstrated visible ability of degrading the cell wall of Laminaria japonica, and biochemical characterization has been performed on some individual enzymes to elucidate its genetic basis. However, it still remains elusive how strain ALW1 successfully breaks down the major cell wall component alginate polysaccharide and colonizes on its marine host. In this study, a mass spectrometry-based quantitative analysis of the extracellular and intracellular proteomes was introduced to elucidate the alginate degradation pathway in ALW1 strain. Mass spectrometry and biochemical assays indicated that strain ALW1 could effectively degrade alginate polysaccharide into disaccharides and trisaccharides within 12 h. Proteome analysis identified 156 and 1,047 proteins exclusively localized in extracellular and intracellular compartments, respectively, with 1,086 protein identities of dual localization. Functional annotation of the identified proteins suggested the involvement of diverse catalytic enzymes and non-catalytic molecules for the cleavage and metabolism of alginate polysaccharide. A simplified pathway was constructed to demonstrate the extracellular digestion, active transport, and intracellular conversion of alginate polysaccharide and its fragmented oligosaccharides, casting a picture of genetic loci controlling alginate catabolism by ALW1 strain. This study aims to provide a guide for utilization and genetic manipulation of the bacterial strain ALW1 for efficient alginate oligosaccharides production by fermentation.
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Affiliation(s)
- Zhipeng Li
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Xiaoyi Huang
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Yuxi Guo
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Chenghao Zhang
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Liang Yang
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Xiping Du
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Hui Ni
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Xuchu Wang
- Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Ministry of Education, Hainan Normal University, Haikou, China
- *Correspondence: Xuchu Wang, ; Yanbing Zhu,
| | - Yanbing Zhu
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
- *Correspondence: Xuchu Wang, ; Yanbing Zhu,
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Li J, He Z, Liang Y, Peng T, Hu Z. Insights into Algal Polysaccharides: A Review of Their Structure, Depolymerases, and Metabolic Pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1749-1765. [PMID: 35124966 DOI: 10.1021/acs.jafc.1c05365] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In recent years, marine macroalgae with extensive biomass have attracted the attention of researchers worldwide. Furthermore, algal polysaccharides have been widely studied in the food, pharmaceutical, and cosmetic fields because of their various kinds of bioactivities. However, there are immense barriers to their application as a result of their high molecular size, poor solubility, hydrocolloid nature, and low physiological activities. Unique polysaccharides, such as laminarin, alginate, fucoidan, agar, carrageenan, porphyran, ulvan, and other complex structural polysaccharides, can be digested by marine bacteria with many carbohydrate-active enzymes (CAZymes) by breaking down the limitation of glycosidic bonds. However, structural elucidation of algal polysaccharides, metabolic pathways, and identification of potential polysaccharide hydrolases that participate in different metabolic pathways remain major obstacles restricting the efficient utilization of algal oligosaccharides. This review focuses on the structure, hydrolase families, metabolic pathways, and potential applications of seven macroalgae polysaccharides. These results will contribute to progressing our understanding of the structure of algal polysaccharides and their metabolic pathways and will be valuable for clearing the way for the compelling utilization of bioactive oligosaccharides.
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Affiliation(s)
- Jin Li
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Zhixiao He
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Yumei Liang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, People's Republic of China
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He XY, Liu NH, Lin CY, Sun ML, Chen XL, Zhang YZ, Zhang YQ, Zhang XY. Description of Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. isolated from Antarctic intertidal sediments. Antonie van Leeuwenhoek 2022; 115:391-405. [PMID: 35022928 DOI: 10.1007/s10482-021-01702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Two Gram-stain-negative, aerobic, non-motile, and rod-shaped bacterial strains, designated SM1352T and A20T, were isolated from intertidal sediments collected from King George Island, Antarctic. They shared 99.8% 16S rRNA gene sequence similarity with each other and had the highest sequence similarity of 98.1% to type strain of Aureibaculum marinum but < 93.4% sequence similarity to those of other known bacterial species. The genomes of strains SM1352T and A20T consisted of 5,108,092 bp and 4,772,071 bp, respectively, with the G + C contents both being 32.0%. They respectively encoded 4360 (including 37 tRNAs and 6 rRNAs) and 4032 (including 36 tRNAs and 5 rRNAs) genes. In the phylogenetic trees based on 16S rRNA gene and single-copy orthologous clusters (OCs), both strains clustered with Aureibaculum marinum and together formed a separate branch within the family Flavobacteriaceae. The ANI and DDH values between the two strains and Aureibaculum marinum BH-SD17T were all below the thresholds for species delineation. The major cellular fatty acids (> 10%) of the two strains included iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH. Their polar lipids predominantly included phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid, and two unidentified lipids. Genomic comparison revealed that both strains possessed much more glycoside hydrolases and sulfatase-rich polysaccharide utilization loci (PULs) than Aureibaculum marinum BH-SD17T. Based on the above polyphasic evidences, strains SM1352T and A20T represent two novel species within the genus Aureibaculum, for which the names Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. are proposed. The type strains are SM1352T (= CCTCC AB 2014243 T = JCM 30335 T) and A20T (= CCTCC AB 2020370 T = KCTC 82503 T), respectively.
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Affiliation(s)
- Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chao-Yi Lin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Mei-Ling Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Pilgaard B, Vuillemin M, Munk L, Holck J, Meier S, Wilkens C, Meyer AS. Discovery of a Novel Glucuronan Lyase System in Trichoderma parareesei. Appl Environ Microbiol 2022; 88:e0181921. [PMID: 34705548 PMCID: PMC8752158 DOI: 10.1128/aem.01819-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/13/2021] [Indexed: 11/20/2022] Open
Abstract
Glucuronan lyases (EC 4.2.2.14) catalyze depolymerization of linear β-(1,4)-polyglucuronic acid (glucuronan). Only a few glucuronan lyases have been characterized until now, most of them originating from bacteria. Here we report the discovery, recombinant production, and functional characterization of the full complement of six glucuronan specific polysaccharide lyases in the necrotic mycoparasite Trichoderma parareesei. The enzymes belong to four different polysaccharide lyase families and have different reaction optima and glucuronan degradation profiles. Four of them showed endo-lytic action and two, TpPL8A and TpPL38A, displayed exo-lytic action. Nuclear magnetic resonance revealed that the monomeric end product from TpPL8A and TpPL38A underwent spontaneous rearrangements to tautomeric forms. Proteomic analysis of the secretomes from T. parareesei growing on pure glucuronan and lyophilized A. bisporus fruiting bodies, respectively, showed secretion of five of the glucuronan lyases and high-performance anion-exchange chromatography with pulsed amperometric detection analysis confirmed the presence of glucuronic acid in the A. bisporus fruiting bodies. By systematic genome annotation of more than 100 fungal genomes and subsequent phylogenetic analysis of the putative glucuronan lyases, we show that glucuronan lyases occur in several ecological and taxonomic groups in the fungal kingdom. Our findings suggest that a diverse repertoire of glucuronan lyases is a common trait among Hypocreales species with mycoparasitic and entomopathogenic lifestyles. IMPORTANCE This paper reports the discovery of a set of six complementary glucuronan lyase enzymes in the mycoparasite Trichoderma parareseei. Apart from the novelty of the discovery of these enzymes in T. parareesei, the key importance of the study is the finding that the majority of these lyases are induced when T. parareesei is inoculated on Basidiomycete cell walls that contain glucuronan. The study also reveals putative glucuronan lyase encoding genes in a wealth of other fungi that furthermore points at fungal cell wall glucuronan being a target C-source for many types of fungi. In a technical context, the findings may lead to controlled production of glucuronan oligomers for advanced pharmaceutical applications and pave the way for development of new fungal biocontrol agents.
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Affiliation(s)
- Bo Pilgaard
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marlene Vuillemin
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Line Munk
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sebastian Meier
- DTU Chemistry, Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Casper Wilkens
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anne S. Meyer
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Kawai S, Hashimoto W. 4-Deoxy-l- erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate. Molecules 2022; 27:338. [PMID: 35056653 PMCID: PMC8778563 DOI: 10.3390/molecules27020338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/31/2022] Open
Abstract
4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not been previously reviewed. Here, we summarize the current understanding of DEH and DEH reductase, with emphasis on (i) the non-enzymatic and enzymatic formation and structure of DEH and its reactivity to specific amino groups, (ii) the molecular identification, classification, function, and structure, as well as the structural determinants for coenzyme specificity of DEH reductase, and (iii) the significance of DEH for biorefinery. Improved understanding of this and related fields should lead to the practical utilization of alginate for biorefinery.
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Affiliation(s)
- Shigeyuki Kawai
- Laboratory for Environmental Biotechnology, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji 611-0011, Kyoto, Japan
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20
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Geng ZQ, Qian DK, Hu ZY, Wang S, Yan Y, van Loosdrecht MCM, Zeng RJ, Zhang F. Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16636-16645. [PMID: 34860015 DOI: 10.1021/acs.est.1c05289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (∼130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner-Doudoroff pathway of alginate via 5-dehydro-4-deoxy-d-glucuronate (DDG) and 3-deoxy-d-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.
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Affiliation(s)
- Zi-Qian Geng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ding-Kang Qian
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhi-Yi Hu
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shuai Wang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yang Yan
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Fang Zhang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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21
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Zeng L, Li J, Cheng Y, Wang D, Gu J, Li F, Han W. Comparison of Biochemical Characteristics, Action Models, and Enzymatic Mechanisms of a Novel Exolytic and Two Endolytic Lyases with Mannuronate Preference. Mar Drugs 2021; 19:md19120706. [PMID: 34940705 PMCID: PMC8705907 DOI: 10.3390/md19120706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Recent explorations of tool-like alginate lyases have been focused on their oligosaccharide-yielding properties and corresponding mechanisms, whereas most were reported as endo-type with α-L-guluronate (G) preference. Less is known about the β-D-mannuronate (M) preference, whose commercial production and enzyme application is limited. In this study, we elucidated Aly6 of Flammeovirga sp. strain MY04 as a novel M-preferred exolytic bifunctional lyase and compared it with AlgLs of Pseudomonas aeruginosa (Pae-AlgL) and Azotobacter vinelandii (Avi-AlgL), two typical M-specific endolytic lyases. This study demonstrated that the AlgL and heparinase_II_III modules play indispensable roles in determining the characteristics of the recombinant exo-type enzyme rAly6, which is preferred to degrade M-enriched substrates by continuously cleaving various monosaccharide units from the nonreducing end, thus yielding various size-defined ΔG-terminated oligosaccharides as intermediate products. By contrast, the endolytic enzymes Pae-rAlgL and Avi-rAlgL varied their action modes specifically against M-enriched substrates and finally degraded associated substrate chains into various size-defined oligosaccharides with a succession rule, changing from ΔM to ΔG-terminus when the product size increased. Furthermore, site-directed mutations and further protein structure tests indicated that H195NHSTW is an active, half-conserved, and essential enzyme motif. This study provided new insights into M-preferring lyases for novel resource discoveries, oligosaccharide preparations, and sequence determinations.
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Affiliation(s)
- Lianghuan Zeng
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine and State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (L.Z.); (J.L.); (D.W.); (F.L.)
- United Post-Graduate Education Base of Shandong University and Jinan Enlighten Biotechnology Co., Ltd., Jinan 250100, China; (Y.C.); (J.G.)
| | - Junge Li
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine and State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (L.Z.); (J.L.); (D.W.); (F.L.)
- United Post-Graduate Education Base of Shandong University and Jinan Enlighten Biotechnology Co., Ltd., Jinan 250100, China; (Y.C.); (J.G.)
| | - Yuanyuan Cheng
- United Post-Graduate Education Base of Shandong University and Jinan Enlighten Biotechnology Co., Ltd., Jinan 250100, China; (Y.C.); (J.G.)
- Department of Food Science and Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China
| | - Dandan Wang
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine and State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (L.Z.); (J.L.); (D.W.); (F.L.)
| | - Jingyan Gu
- United Post-Graduate Education Base of Shandong University and Jinan Enlighten Biotechnology Co., Ltd., Jinan 250100, China; (Y.C.); (J.G.)
| | - Fuchuan Li
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine and State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (L.Z.); (J.L.); (D.W.); (F.L.)
| | - Wenjun Han
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine and State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (L.Z.); (J.L.); (D.W.); (F.L.)
- United Post-Graduate Education Base of Shandong University and Jinan Enlighten Biotechnology Co., Ltd., Jinan 250100, China; (Y.C.); (J.G.)
- Activity Biotechnology Co., Ltd., Jinan 250100, China
- Correspondence: ; Tel.: +86-15763908639
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22
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Rhein-Knudsen N, Guan C, Mathiesen G, Horn SJ. Expression and production of thermophilic alginate lyases in Bacillus and direct application of culture supernatant for seaweed saccharification. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Nishiyama R, Ojima T, Ohnishi Y, Kumaki Y, Aizawa T, Inoue A. An oxidative metabolic pathway of 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEHU) from alginate in an alginate-assimilating bacterium. Commun Biol 2021; 4:1254. [PMID: 34728789 PMCID: PMC8563752 DOI: 10.1038/s42003-021-02786-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/14/2021] [Indexed: 11/22/2022] Open
Abstract
Alginate-assimilating bacteria degrade alginate into an unsaturated monosaccharide, which is converted into 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEHU). DEHU is reduced to 2-keto-3-deoxy-D-gluconate by a DEHU-specific reductase using NAD(P)H. This is followed by pyruvate production via the Entner-Doudoroff pathway. Previously, we identified FlRed as a DEHU reductase in an alginate-assimilating bacterium, Flavobacterium sp. strain UMI-01. Here, we showed that FlRed can also catalyze the oxidation of DEHU with NAD+, producing 2-keto-3-deoxy-D-glucarate (KDGR). FlRed showed a predilection for NADH and NAD+ over NADPH and NADP+, respectively, and the Km value for NADH was approximately 2.6-fold less than that for NAD+. Furthermore, we identified two key enzymes, FlDet and FlDeg, for KDGR catabolism. FlDet was identified as an enzyme of the ribonuclease activity regulator A family, which converts KDGR to α-ketoglutaric semialdehyde (α-KGSA). FlDeg, a type II α-KGSA dehydrogenase, generated α-ketoglutaric acid by oxidizing the aldehyde group of α-KGSA using NAD(P)+. Consequently, unlike the conventional DEHU reduction pathway, DEHU can be directly converted to α-ketoglutaric acid without consuming NAD(P)H. Alginate upregulated the expression of not only FlRed and two enzymes of the DEHU-reduction pathway, but also FlDet and FlDeg. These results revealed dual pathways of DEHU metabolism involving reduction or oxidation by FlRed.
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Affiliation(s)
- Ryuji Nishiyama
- grid.39158.360000 0001 2173 7691Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido Japan
| | - Takao Ojima
- grid.39158.360000 0001 2173 7691Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido Japan
| | - Yuki Ohnishi
- grid.39158.360000 0001 2173 7691Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Yasuhiro Kumaki
- grid.39158.360000 0001 2173 7691Faculty of Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Tomoyasu Aizawa
- grid.39158.360000 0001 2173 7691Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Akira Inoue
- grid.39158.360000 0001 2173 7691Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido Japan
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24
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Xu F, Cha QQ, Zhang YZ, Chen XL. Degradation and Utilization of Alginate by Marine Pseudoalteromonas: a Review. Appl Environ Microbiol 2021; 87:e0036821. [PMID: 34160244 PMCID: PMC8357284 DOI: 10.1128/aem.00368-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Alginate, which is mainly produced by brown algae and decomposed by heterotrophic bacteria, is an important marine organic carbon source. The genus Pseudoalteromonas contains diverse forms of heterotrophic bacteria that are widely distributed in marine environments and are an important group in alginate degradation. In this review, the diversity of alginate-degrading Pseudoalteromonas is introduced, and the characteristics of Pseudoalteromonas alginate lyases, including their sequences, enzymatic properties, structures, and catalytic mechanisms, and the synergistic effect of Pseudoalteromonas alginate lyases on alginate degradation are introduced. The acquisition of the alginate degradation capacity and the alginate utilization pathways of Pseudoalteromonas are also introduced. This paper provides a comprehensive overview of alginate degradation by Pseudoalteromonas, which will contribute to the understanding of the degradation and recycling of marine algal polysaccharides driven by marine bacteria.
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Affiliation(s)
- Fei Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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25
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Zhang L, Li X, Zhang X, Li Y, Wang L. Bacterial alginate metabolism: an important pathway for bioconversion of brown algae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:158. [PMID: 34275475 PMCID: PMC8286568 DOI: 10.1186/s13068-021-02007-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Brown macroalgae have attracted great attention as an alternative feedstock for biorefining. Although direct conversion of ethanol from alginates (major components of brown macroalgae cell walls) is not amenable for industrial production, significant progress has been made not only on enzymes involved in alginate degradation, but also on metabolic pathways for biorefining at the laboratory level. In this article, we summarise recent advances on four aspects: alginate, alginate lyases, different alginate-degrading systems, and application of alginate lyases and associated pathways. This knowledge will likely inspire sustainable solutions for further application of both alginate lyases and their associated pathways.
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Affiliation(s)
- Lanzeng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiyue Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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26
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Li Q, Zheng L, Guo Z, Tang T, Zhu B. Alginate degrading enzymes: an updated comprehensive review of the structure, catalytic mechanism, modification method and applications of alginate lyases. Crit Rev Biotechnol 2021; 41:953-968. [PMID: 34015998 DOI: 10.1080/07388551.2021.1898330] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Alginate, a kind of linear acidic polysaccharide, consists of α-L-guluronate (G) and β-D-mannuronate (M). Both alginate and its degradation products (alginate oligosaccharides) possess abundant biological activities such as antioxidant activity, antitumor activity, and antimicrobial activity. Therefore, alginate and alginate oligosaccharides have great value in food, pharmaceutical, and agricultural fields. Alginate lyase can degrade alginate into alginate oligosaccharides via the β-elimination reaction. It plays an important role in marine carbon recycling and the deep utilization of brown algae. Elucidating the structural features of alginate lyase can improve our knowledge of its catalytic mechanisms. With the development of structural analysis techniques, increasing numbers of alginate lyases have been characterized at the structural level. Hence, it is essential and helpful to summarize and discuss the up-to-date findings. In this review, we have summarized progress on the structural features and the catalytic mechanisms of alginate lyases. Furthermore, the molecular modification strategies and the applications of alginate lyases have also been discussed. This comprehensive information should be helpful to expand the applications of alginate lyases.
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Affiliation(s)
- Qian Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ling Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zilong Guo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Tiancheng Tang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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27
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Zhang R. The Cupin Protein Pac13 is Suggested by the Data to Be a Homodimer. Angew Chem Int Ed Engl 2021; 59:12580-12583. [PMID: 32691958 DOI: 10.1002/anie.201811240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/15/2019] [Indexed: 02/05/2023]
Abstract
Cupin proteins share a double-stranded β-helix fold, form one of the largest protein superfamilies, and possess remarkable functional diversity. They usually exist in homooligomeric states. Goss and co-workers recently reported that the cupin protein Pac13, which is a dehydratase that mediates the formation of the 3'-deoxy nucleoside of pacidamycins, is an unusual small monomer. However, a careful analysis of the biophysical and structural data provided by the authors suggests that Pac13 is in fact a homodimer, similar to many other cupin proteins.
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Affiliation(s)
- Rundong Zhang
- Department of Ophthalmology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
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28
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Inoue A, Ojima T. Functional identification of the 4-deoxy-L-erythro-5-hexoseulose uronate reductase from a brown alga, Saccharina japonica. Biochem Biophys Res Commun 2021; 545:112-118. [PMID: 33548623 DOI: 10.1016/j.bbrc.2021.01.090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/25/2021] [Indexed: 11/23/2022]
Abstract
We previously reported the alginate lyase, SjAly, from a brown alga, Saccharina japonica, providing the first experimental evidence for a functional alginate-degradation enzyme in brown algae. 4-deoxy-L-erythro-5-hexoseulose uronate (DEHU), derived from an unsaturated monosaccharide, was identified as the minimum degradation product produced by SjAly-mediated lysis of alginate. DEHU was hitherto reported to be reduced to 2-keto-3-deoxy-gluconate (KDG) by a DEHU-specific reductase with NAD(P)H in alginate-assimilating organisms and its metabolism in alginate-producing organisms is unknown. Here, we report the functional identification of a DEHU reductase, SjRed, in S. japonica. Among the 14 tested compounds, only DEHU was used as a substrate and was converted to KDG in the presence of NADPH. Optimum temperature, pH, and KCl concentration required for SjRed activity were determined to be 25 °C, 7.2, and 100 mM, respectively. SjRed consists of 341 amino acid residues and is proposed to be a member of the aldo-keto reductase superfamily. Sequencing of SjRed revealed that it is composed of at least three exons. These results indicate the existence of an enzyme that reduces DEHU to KDG in S. japonica. This is the first report on the functional identification of a DEHU-reductase in alginate-producing organisms.
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Affiliation(s)
- Akira Inoue
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan.
| | - Takao Ojima
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
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29
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Park S, Cho SW, Lee Y, Choi M, Yang J, Lee H, Seo SW. Engineering Vibrio sp. SP1 for the production of carotenoids directly from brown macroalgae. Comput Struct Biotechnol J 2021; 19:1531-1540. [PMID: 33815690 PMCID: PMC7994440 DOI: 10.1016/j.csbj.2021.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 11/18/2022] Open
Abstract
Macroalgae is regarded as a promising third-generation marine biomass that can be utilized as a sustainable feedstock for bio-industry due to the high sugar level and absence of lignin. Alginate, composed of 1,4-linked D-mannuronate (M) and L-guluronate (G), is one of the major carbohydrates in brown macroalgae. It is difficult to be assimilated by most industrial microorganisms. Therefore, developing engineered microorganisms that can utilize alginate as a feedstock in order to produce natural products from marine biomass is critical. In this study, we isolated, characterized, and sequenced Vibrio sp. SP1 which rapidly grows using alginate as a sole carbon source. We further engineered this strain by introducing genes encoding enzymes under the control of synthetic expression cassettes to produce lycopene and β-carotene which are attractive phytochemicals owing to the antioxidant property. We confirmed that the engineered Vibrio sp. SP1 could successfully produce 2.13 ± 0.37 mg L-1 of lycopene, 2.98 ± 0.43 mg L-1 of β -carotene, respectively, from 10 g L-1 of alginate as a sole carbon source. Furthermore, our engineered strain could directly convert 60 g L-1 of brown macroalgae Sargassum fusiforme into 1.23 ± 0.21 mg L-1 of lycopene without any pretreatment which had been vitally required for the previous productions. As the first demonstrated strain to produce high-value product from Sargassum, Vibrio sp. SP1 is evaluated to be a desirable platform for the brown macroalgae-based biorefinery.
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Affiliation(s)
- Sungwoo Park
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Sung Won Cho
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Yungyu Lee
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Mincheol Choi
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hojun Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Bio-MAX Institute Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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30
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Furusawa G, Azami NA, Teh AH. Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4. PeerJ 2021; 9:e10929. [PMID: 33732545 PMCID: PMC7953866 DOI: 10.7717/peerj.10929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. METHODS To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. RESULTS The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate.
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Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Nor Azura Azami
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
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Alginate Degradation: Insights Obtained through Characterization of a Thermophilic Exolytic Alginate Lyase. Appl Environ Microbiol 2021; 87:AEM.02399-20. [PMID: 33397696 DOI: 10.1128/aem.02399-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/19/2020] [Indexed: 01/07/2023] Open
Abstract
Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a thermostable alginate lyase that belongs to polysaccharide lyase family 17 (PL17) and was derived from an Arctic Mid-Ocean Ridge (AMOR) metagenomics data set. This enzyme, AMOR_PL17A, is a thermostable exolytic oligoalginate lyase (EC 4.2.2.26), which can degrade alginate, poly-β-d-mannuronate, and poly-α-l-guluronate within a broad range of pHs, temperatures, and salinity conditions. Site-directed mutagenesis showed that tyrosine Y251, previously suggested to act as a catalytic acid, indeed is essential for catalysis, whereas mutation of tyrosine Y446, previously proposed to act as a catalytic base, did not affect enzyme activity. The observed reaction products are protonated and deprotonated forms of the 4,5-unsaturated uronic acid monomer, Δ, two hydrates of DEH (4-deoxy-l-erythro-5-hexulosuronate), which are formed after ring opening, and, finally, two epimers of a 5-member hemiketal called 4-deoxy-d-manno-hexulofuranosidonate (DHF), formed through intramolecular cyclization of hydrated DEH. The detection and nuclear magnetic resonance (NMR) assignment of these hemiketals refine our current understanding of alginate degradation.IMPORTANCE The potential markets for seaweed-derived products and seaweed processing technologies are growing, yet commercial enzyme cocktails for complete conversion of seaweed to fermentable sugars are not available. Such an enzyme cocktail would require the catalytic properties of a variety of different enzymes, where fucoidanases, laminarinases, and cellulases together with endo- and exo-acting alginate lyases would be the key enzymes. Here, we present an exo-acting alginate lyase that efficiently produces monomeric sugars from alginate. Since it is only the second characterized exo-acting alginate lyase capable of degrading alginate at a high industrially relevant temperature (≥60°C), this enzyme may be of great biotechnological and industrial interest. In addition, in-depth NMR-based structural elucidation revealed previously undescribed rearrangement products of the unsaturated monomeric sugars generated from exo-acting lyases. The insight provided by the NMR assignment of these products facilitates future assessment of product formation by alginate lyases.
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Cha QQ, Wang XJ, Ren XB, Li D, Wang P, Li PY, Fu HH, Zhang XY, Chen XL, Zhang YZ, Xu F, Qin QL. Comparison of Alginate Utilization Pathways in Culturable Bacteria Isolated From Arctic and Antarctic Marine Environments. Front Microbiol 2021; 12:609393. [PMID: 33584613 PMCID: PMC7874173 DOI: 10.3389/fmicb.2021.609393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Alginate, mainly derived from brown algae, is an important carbon source that can support the growth of marine microorganisms in the Arctic and Antarctic regions. However, there is a lack of systematic investigation and comparison of alginate utilization pathways in culturable bacteria from both polar regions. In this study, 88 strains were isolated from the Arctic and Antarctic regions, of which 60 strains could grow in the medium with alginate as the sole carbon source. These alginate-utilizing strains belong to 9 genera of the phyla Proteobacteria and Bacteroidetes. The genomes of 26 alginate-utilizing strains were sequenced and genomic analyses showed that they all contain the gene clusters related to alginate utilization. The alginate transport systems of Proteobacteria differ from those of Bacteroidetes and there may be unique transport systems among different genera of Proteobacteria. The biogeographic distribution pattern of alginate utilization genes was further investigated. The alginate utilization genes are found to cluster according to bacterial taxonomy rather than geographic location, indicating that the alginate utilization genes do not evolve independently in both polar regions. This study systematically illustrates the alginate utilization pathways in culturable bacteria from the Arctic and Antarctic regions, shedding light into the distribution and evolution of alginate utilization pathways in polar bacteria.
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Affiliation(s)
- Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Dong Li
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Separation and quantification of 2-keto-3-deoxy-gluconate (KDG) a major metabolite in pectin and alginate degradation pathways. Anal Biochem 2020; 619:114061. [PMID: 33285123 DOI: 10.1016/j.ab.2020.114061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/21/2022]
Abstract
A rapid and sensitive High Performance Liquid Chromatography (HPLC) method with photometric and fluorescence detection is developed for routine analysis of 2-Keto-3-deoxy-gluconate (KDG), a catabolite product of pectin and alginate. These polysaccharides are primary-based compounds for biofuel production and for generation of high-value-added products. HPLC is performed, after derivatization of the 2-oxo-acid groups of the metabolite with o-phenylenediamine (oPD), using a linear gradient of trifluoroacetic acid and acetonitrile. Quantification is accomplished with an internal standard method. The gradient is optimized to distinguish KDG from its close structural analogues such as 5-keto-4-deoxyuronate (DKI) and 2,5-diketo-3-deoxygluconate (DKII). The proposed method is simple, highly sensitive and accurate for time course analysis of pectin or alginate degradation.
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Dudek M, Dieudonné A, Jouanneau D, Rochat T, Michel G, Sarels B, Thomas F. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Nucleic Acids Res 2020; 48:7786-7800. [PMID: 32585009 PMCID: PMC7641319 DOI: 10.1093/nar/gkaa533] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.
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Affiliation(s)
- Magda Dudek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anissa Dieudonné
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Benoit Sarels
- Sorbonne Université, CNRS, Laboratoire Jacques-Louis Lions, Université de Paris, 75252 Paris, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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Moriya H, Takita Y, Matsumoto A, Yamahata Y, Nishimukai M, Miyazaki M, Shimoi H, Kawai SJ, Yamada M. Cobetia sp. Bacteria, Which Are Capable of Utilizing Alginate or Waste Laminaria sp. for Poly(3-Hydroxybutyrate) Synthesis, Isolated From a Marine Environment. Front Bioeng Biotechnol 2020; 8:974. [PMID: 32984275 PMCID: PMC7479843 DOI: 10.3389/fbioe.2020.00974] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 11/13/2022] Open
Abstract
We isolated the Cobetia sp. strains IU 180733JP01 (5-11-6-3) and 190790JP01 (5-25-4-2) from seaweeds and showed that both strains accumulate poly(3-hydroxybutyrate) [P(3HB)] homopolymer in a nitrogen-limiting mineral salt medium containing alginate as a sole carbon source. Genome sequence analysis of the isolated strains showed that they have putative genes which encode enzymes relevant to alginate assimilation and P(3HB) synthesis, and the putative alginate-assimilating genes formed a cluster. Investigation of the optimum culture conditions for high accumulation of P(3HB) showed that when the 5-11-6-3 strain was cultured in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and 3% (w/v) alginate as a sole carbon source for 2 days, the P(3HB) content and P(3HB) production reached 62.1 ± 3.4 wt% and 3.11 ± 0.16 g/L, respectively. When the 5-25-4-2 strain was cultured in a nitrogen-limiting mineral salt medium (pH 4.0) containing 5% NaCl and 3% (w/v) alginate for 2 days, the P(3HB) content and P(3HB) production reached 56.9 ± 2.1 wt% and 2.67 ± 0.11 g/L, respectively. Moreover, the 5-11-6-3 strain also produced P(3HB) in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and freeze-dried and crushed waste Laminaria sp., which is classified into brown algae and contains alginate abundantly. The resulting P(3HB) content and P(3HB) productivity were 13.5 ± 0.13 wt% and 3.99 ± 0.15 mg/L/h, respectively. Thus, we demonstrated the potential application of the isolated strains to a simple P(3HB) production process from seaweeds without chemical hydrolysis and enzymatic saccharification.
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Affiliation(s)
- Hiroki Moriya
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Yuto Takita
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Akira Matsumoto
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Yuki Yamahata
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Megumi Nishimukai
- Department of Animal Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Hitoshi Shimoi
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Sung-Jin Kawai
- New Field Pioneering Division, New Value Creation Center, Toyota Boshoku Corporation, Kariya, Japan
| | - Miwa Yamada
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
- Education and Research on Sanriku Fishery Industry Department, Organization for Revitalization of the Sanriku Region and Regional Development, Iwate University, Morioka, Japan
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Huang Z, Petersen JM, Martijn J, Ettema TJG, Shao Z. A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:387-395. [PMID: 32307920 DOI: 10.1111/1758-2229.12845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.
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Affiliation(s)
- Zhaobin Huang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
| | - Jillian M Petersen
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
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37
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Zhang R. The Cupin Protein Pac13 is Suggested by the Data to Be a Homodimer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201811240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rundong Zhang
- Department of Ophthalmology State Key Laboratory of Biotherapy West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu 610041 P. R. China
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38
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Li S, Wang L, Jung S, Lee BS, He N, Lee MS. Biochemical Characterization of a New Oligoalginate Lyase and Its Biotechnological Application in Laminaria japonica Degradation. Front Microbiol 2020; 11:316. [PMID: 32210931 PMCID: PMC7076127 DOI: 10.3389/fmicb.2020.00316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022] Open
Abstract
Oligoalginate lyases catalyze the degradation of alginate polymers and oligomers into monomers, a prerequisite for biotechnological utilizing alginate. In this study, we report the cloning, expression and biochemical characterization of a new polysaccharide lyase (PL) family 17 oligoalginate lyase, OalV17, from the marine bacterium Vibrio sp. SY01. The recombinant OalV17 showed metal ion independent and detergent resistant properties. Furthermore, OalV17 is an exo-type enzyme that yields alginate monomers as the main product and recognizes alginate disaccharides as the minimal substrate. Site-directed mutagenesis followed by kinetic analysis indicates that the residue Arg231 plays a key role in substrate specificity. Furthermore, a rapid and efficient alginate monomer-producing method was developed directly from Laminaria japonica. These results suggest that OalV17 is a potential candidate for saccharification of alginate.
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Affiliation(s)
- Shangyong Li
- School of Basic Medicine, Qingdao University, Qingdao, China.,Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
| | - Linna Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Samil Jung
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
| | - Beom Suk Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
| | - Ningning He
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Myeong-Sok Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
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40
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Hettle AG, Hobbs JK, Pluvinage B, Vickers C, Abe KT, Salama-Alber O, McGuire BE, Hehemann JH, Hui JPM, Berrue F, Banskota A, Zhang J, Bottos EM, Van Hamme J, Boraston AB. Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species. Commun Biol 2019; 2:474. [PMID: 31886414 PMCID: PMC6923384 DOI: 10.1038/s42003-019-0721-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023] Open
Abstract
Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-carrageenan specific polysaccharide utilization locus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.
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Affiliation(s)
- Andrew G. Hettle
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Joanne K. Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Chelsea Vickers
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: School of Biological Sciences, Victoria University, PO Box 600, Wellington, 6012 New Zealand
| | - Kento T. Abe
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Ave, Rm 992, Toronto, ON M5G1X5 Canada
| | - Orly Salama-Alber
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Bailey E. McGuire
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Jan-Hendrik Hehemann
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: Marum and Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Joseph P. M. Hui
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Fabrice Berrue
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Arjun Banskota
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Junzeng Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Eric M. Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8 Canada
| | - Jonathan Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8 Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
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Nakata S, Murata K, Hashimoto W, Kawai S. Uncovering the reactive nature of 4-deoxy-L-erythro-5-hexoseulose uronate for the utilization of alginate, a promising marine biopolymer. Sci Rep 2019; 9:17147. [PMID: 31748627 PMCID: PMC6868183 DOI: 10.1038/s41598-019-53597-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 11/01/2019] [Indexed: 02/08/2023] Open
Abstract
Alginate is a linear polyuronate in brown macroalgae. It is also a promising marine biopolymer that can be degraded by exo-type alginate lyase into an unsaturated uronate that is non-enzymatically or enzymatically converted to 4-deoxy-L-erythro-5-hexoseulose uronate (DEH). In a bioengineered yeast Saccharomyces cerevisiae (DEH++) strain that utilizes DEH, DEH is not only an important physiological metabolite but also a promising carbon source for biorefinery systems. In this study, we uncovered the essential chemical nature of DEH. In particular, we showed that DEH non-enzymatically reacts with specific amino groups in Tris, ammonium salts [(NH4)2SO4 and NH4Cl], and certain amino acids (e.g., Gly, Ser, Gln, Thr, and Lys) at 30 °C and forms other compounds, one of which we tentatively named DEH-related product-1 (DRP-1). In contrast, Asn, Met, Glu, and Arg were almost inert and Ala, Pro, Leu, Ile, Phe, Val, and Asp, as well as sodium nitrate (NaNO3), were inert in the presence of DEH. Some of the above amino acids (Asn, Glu, Ala, Pro, Phe, and Asp) were suitable nitrogen sources for the DEH++ yeast strain, whereas ammonium salts and Ser, Gln, and Thr were poor nitrogen sources owing to their high reactivity to DEH. Nutrient-rich YP medium with 1% (w/v) Yeast extract and 2% (w/v) Tryptone, as well as 10-fold diluted YP medium, could also be effectively used as nitrogen sources. Finally, we identified DRP-1 as a 2-furancarboxylic acid and showed that it has a growth-inhibitory effect on the DEH++ yeast strain. These results show the reactive nature of DEH and suggest a basis for selecting nitrogen sources for use with DEH and alginate in biorefineries. Our results also provide insight into the physiological utilization of DEH. The environmental source of 2-furancarboxylic acid is also discussed.
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Affiliation(s)
- Shota Nakata
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Kousaku Murata
- Faculty of Science and Engineering, Department of Life Science, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, 572-8508, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Shigeyuki Kawai
- Laboratory for Environmental Biotechnology, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
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Hugouvieux-Cotte-Pattat N, Jacot-des-Combes C, Briolay J. Genomic characterization of a pectinolytic isolate of Serratia oryzae isolated from lake water. J Genomics 2019; 7:64-72. [PMID: 31719848 PMCID: PMC6831795 DOI: 10.7150/jgen.38365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/16/2019] [Indexed: 11/05/2022] Open
Abstract
Only one isolate of Serratia oryzae, the type strain J11-6T has been characterized up to now. This strain was found in the endophytic bacterial flora of rice. As part of an ongoing investigation into pectinolytic bacteria present in lake water in France, a few Serratia strains were isolated, including S32 and J9 identified as new strains of S. oryzae. The genome of strain S32 consists of a circular chromosome of 4,810,389 bp that contains 4,584 protein-coding genes. The genome of S32, as well as those of the type strain J11-6T, contains several genes involved in pectin degradation and in the intracellular assimilation of pectin oligomers. The specific detection of enzyme activities confirmed that strain S32 secretes functional pectinases and that it also produces extracellular cellulase and protease activities. The ability to produce plant cell wall degrading enzymes shows that S. oryzae shares characteristics of plant associated bacteria, including phytopathogens.
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Affiliation(s)
- Nicole Hugouvieux-Cotte-Pattat
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, UMR5240 Microbiologie Adaptation et Pathogénie, F-69621Villeurbanne, France
| | - Cécile Jacot-des-Combes
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, plateforme DTAMB, FR3728 BioEnviS, F-69621Villeurbanne, France
| | - Jérôme Briolay
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, plateforme DTAMB, FR3728 BioEnviS, F-69621Villeurbanne, France
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43
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Jones DR, McLean R, Hobbs JK, Abbott DW. A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase. J Struct Biol 2019; 207:279-286. [PMID: 31200020 DOI: 10.1016/j.jsb.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Yersinia enterocolitica is a pectinolytic zoonotic foodborne pathogen, the genome of which contains pectin-binding proteins and several different classes of pectinases, including polysaccharide lyases (PLs) and an exopolygalacturonase. These proteins operate within a coordinated pathway to completely saccharify homogalacturonan (HG). Polysaccharide lyase family 2 (PL2) is divided into two major subfamilies that are broadly-associated with contrasting 'endolytic' (PL2A) or 'exolytic' (PL2B) activities on HG. In the Y. enterocolitica genome, the PL2A gene is adjacent to an independent carbohydrate binding module from family 32 (YeCBM32), which possesses a N-terminal secretion tag and is known to specifically bind HG. Independent CBMs are rare in nature and, most commonly, are fused to enzymes in order to potentiate catalysis. The unconventional gene architecture of YePL2A and YeCBM32, therefore, may represent an ancestral relic of a fission event that decoupled PL2A from its cognate CBM. To provide further insight into the evolution of this pectinolytic locus and the molecular basis of HG depolymerisation within Y. enterocolitica, we have resurrected a YePL2A-YeCBM32 chimera and demonstrated that the extant PL2A digests HG more efficiently. In addition, we have engineered a tryptophan from the active site of the exolytic YePL2B into YePL2A (YePL2A-K291W) and demonstrated, using X-ray crystallography of substrate complexes, that it is a structural determinant of exo-activity within the PL2 family. In this manner, surrogate structural platforms may assist in the study of phylogenetic relationships informed by extant and resurrected sequences, and can be used to overcome challenging structural problems within carbohydrate active enzyme families.
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Affiliation(s)
- Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
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Kuivanen J, Biz A, Richard P. Microbial hexuronate catabolism in biotechnology. AMB Express 2019; 9:16. [PMID: 30701402 PMCID: PMC6353982 DOI: 10.1186/s13568-019-0737-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
The most abundant hexuronate in plant biomass is D-galacturonate. D-Galacturonate is the main constituent of pectin. Pectin-rich biomass is abundantly available as sugar beet pulp or citrus processing waste and is currently mainly used as cattle feed. Other naturally occurring hexuronates are D-glucuronate, L-guluronate, D-mannuronate and L-iduronate. D-Glucuronate is a constituent of the plant cell wall polysaccharide glucuronoxylan and of the algal polysaccharide ulvan. Ulvan also contains L-iduronate. L-Guluronate and D-mannuronate are the monomers of alginate. These raw materials have the potential to be used as raw material in biotechnology-based production of fuels or chemicals. In this communication, we will review the microbial pathways related to these hexuronates and their potential use in biotechnology.
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Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep 2019; 9:364. [PMID: 30674920 PMCID: PMC6344544 DOI: 10.1038/s41598-018-36247-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Ectoine synthase (EctC) is the signature enzyme for the production of ectoine, a compatible solute and chemical chaperone widely synthesized by bacteria as a cellular defense against the detrimental effects of osmotic stress. EctC catalyzes the last step in ectoine synthesis through cyclo-condensation of the EctA-formed substrate N-gamma-acetyl-L-2,4-diaminobutyric acid via a water elimination reaction. We have biochemically and structurally characterized the EctC enzyme from the thermo-tolerant bacterium Paenibacillus lautus (Pl). EctC is a member of the cupin superfamily and forms dimers, both in solution and in crystals. We obtained high-resolution crystal structures of the (Pl)EctC protein in forms that contain (i) the catalytically important iron, (ii) iron and the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid, and (iii) iron and the enzyme reaction product ectoine. These crystal structures lay the framework for a proposal for the EctC-mediated water-elimination reaction mechanism. Residues involved in coordinating the metal, the substrate, or the product within the active site of ectoine synthase are highly conserved among a large group of EctC-type proteins. Collectively, the biochemical, mutational, and structural data reported here yielded detailed insight into the structure-function relationship of the (Pl)EctC enzyme and are relevant for a deeper understanding of the ectoine synthase family as a whole.
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46
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Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, Dittmar T, Freese HM, Becher D, Simon M, Wietz M. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. THE ISME JOURNAL 2019; 13:92-103. [PMID: 30116038 PMCID: PMC6298977 DOI: 10.1038/s41396-018-0252-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/08/2022]
Abstract
Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct 'carbohydrate utilization types' with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alexandra Dürwald
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Silvia Vidal-Melgosa
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Jan-Hendrik Hehemann
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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Biochemical Reconstruction of a Metabolic Pathway from a Marine Bacterium Reveals Its Mechanism of Pectin Depolymerization. Appl Environ Microbiol 2018; 85:AEM.02114-18. [PMID: 30341080 DOI: 10.1128/aem.02114-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
Pectin is a complex uronic acid-containing polysaccharide typically found in plant cell walls, though forms of pectin are also found in marine diatoms and seagrasses. Genetic loci that target pectin have recently been identified in two phyla of marine bacteria. These loci appear to encode a pectin saccharification pathway that is distinct from the canonical pathway typically associated with phytopathogenic terrestrial bacteria. However, very few components of the marine pectin metabolism pathway have been experimentally validated. Here, we biochemically reconstructed the pectin saccharification pathway from a marine Pseudoalteromonas sp. in vitro and show that it results in the production of galacturonate and the key metabolic intermediate 5-keto-4-deoxyuronate (DKI). We demonstrate the sequential de-esterification and depolymerization of pectin into oligosaccharides and the synergistic action of glycoside hydrolases (GHs) to fully degrade these oligosaccharides into monosaccharides. Furthermore, we show that this pathway relies on enzymes belonging to GH family 105 to carry out the equivalent chemistry afforded by an exolytic polysaccharide lyase (PL) and KdgF in the canonical pectin pathway. Finally, we synthesize our findings into a model of marine pectin degradation and compare it with the canonical pathway. Our results underline the shifting view of pectin as a solely terrestrial polysaccharide and highlight the importance of marine pectin as a carbon source for suitably adapted marine heterotrophs. This alternate pathway has the potential to be exploited in the growing field of biofuel production from plant waste.IMPORTANCE Marine polysaccharides, found in the cell walls of seaweeds and other marine macrophytes, represent a vast sink of photosynthetically fixed carbon. As such, their breakdown by marine microbes contributes significantly to global carbon cycling. Pectin is an abundant polysaccharide found in the cell walls of terrestrial plants, but it has recently been reported that some marine bacteria possess the genetic capacity to degrade it. In this study, we biochemically characterized seven key enzymes from a marine bacterium that, together, fully degrade the backbone of pectin into its constituent monosaccharides. Our findings highlight the importance of pectin as a marine carbon source available to bacteria that possess this pathway. The characterized enzymes also have the potential to be utilized in the production of biofuels from plant waste.
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Gobet A, Barbeyron T, Matard-Mann M, Magdelenat G, Vallenet D, Duchaud E, Michel G. Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9 T to Adapt to Macroalgal Niches. Front Microbiol 2018; 9:2740. [PMID: 30524390 PMCID: PMC6262041 DOI: 10.3389/fmicb.2018.02740] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/26/2018] [Indexed: 01/16/2023] Open
Abstract
About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9T (ATCC 43555T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.
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Affiliation(s)
- Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Maria Matard-Mann
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France.,Amadéite SAS, "Pôle Biotechnologique" du Haut du Bois, Bréhan, France
| | - Ghislaine Magdelenat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - David Vallenet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Eric Duchaud
- VIM, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
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Lee EJ, Lee OK, Lee EY. Identification of 4-Deoxy-L-Etychro-Hexoseulose Uronic Acid Reductases in an Alginolytic Bacterium Vibrio splendidus and their Uses for L-Lactate Production in an Escherichia coli Cell-Free System. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:410-423. [PMID: 29532336 DOI: 10.1007/s10126-018-9805-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/27/2018] [Indexed: 12/17/2023]
Abstract
4-Deoxy-L-erythro-hexoseulose uronic acid (DEH) reductase is a key enzyme in alginate utilizing metabolism, but the number of characterized DEH reductase is quite limited. In this study, novel two DEH reductases, VsRed-1 and VsRed-2, were identified in marine bacterium Vibrio splendidus, and the recombinant enzymes were expressed in an Escherichia coli system and purified by Ni-NTA chromatography. The optimal pH and temperature of the recombinant VsRed-1 and VsRed-2 were pH 7.5, 30 °C, and pH 7.0, 35 °C, respectively. The specific activities of VsRed-1 (776 U/mg for NADH) and VsRed-2 (176 U/mg for NADPH) were the highest among the DEH reductases reported so far. We also demonstrated that DEH could be converted to L-lactate with a yield of 76.7 and 81.9% in E. coli cell-free system containing VsRed-1 and VsRed-2 enzymes, respectively, indicating that two DEH reductases can be employed for production of biofuels and bio-chemicals from brown macroalgae biomass.
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Affiliation(s)
- Eun Jeong Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, South Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, South Korea.
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50
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The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme. Structure 2018; 26:747-758.e4. [PMID: 29681469 DOI: 10.1016/j.str.2018.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/26/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022]
Abstract
Sulfatases play a biologically important role by cleaving sulfate groups from molecules. They can be identified on the basis of signature sequences within their primary structures, and the largest family, S1, has predictable features that contribute specifically to the recognition and catalytic removal of sulfate groups. However, despite advances in the prediction and understanding of S1 sulfatases, a major question regards the molecular determinants that drive substrate recognition beyond the targeted sulfate group. Here, through analysis of an endo-4S-ι-carrageenan sulfatase (PsS1_19A) from Pseudoalteromonas sp. PS47, particularly X-ray crystal structures in complex with intact substrates, we show that specific recognition of the substrate leaving group components, in this case carbohydrate, provides the enzyme with specificity for its substrate. On the basis of these results we propose a catalytic subsite nomenclature that we anticipate will form a general foundation for understanding and describing the molecular basis of substrate recognition by sulfatases.
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